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Pacot L, Girish M, Knight S, Spurlock G, Varghese V, Ye M, Thomas N, Pasmant E, Upadhyaya M. Correlation between large rearrangements and patient phenotypes in NF1 deletion syndrome: an update and review. BMC Med Genomics 2024; 17:73. [PMID: 38448973 PMCID: PMC10919053 DOI: 10.1186/s12920-024-01843-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/01/2024] [Indexed: 03/08/2024] Open
Abstract
About 5-10% of neurofibromatosis type 1 (NF1) patients exhibit large genomic germline deletions that remove the NF1 gene and its flanking regions. The most frequent NF1 large deletion is 1.4 Mb, resulting from homologous recombination between two low copy repeats. This "type-1" deletion is associated with a severe clinical phenotype in NF1 patients, with several phenotypic manifestations including learning disability, a much earlier development of cutaneous neurofibromas, an increased tumour risk, and cardiovascular malformations. NF1 adjacent co-deleted genes could act as modifier loci for the specific clinical manifestations observed in deleted NF1 patients. Furthermore, other genetic modifiers (such as CNVs) not located at the NF1 locus could also modulate the phenotype observed in patients with large deletions. In this study, we analysed 22 NF1 deletion patients by genome-wide array-CGH with the aim (1) to correlate deletion length to observed phenotypic features and their severity in NF1 deletion syndrome, and (2) to identify whether the deletion phenotype could also be modulated by copy number variations elsewhere in the genome. We then review the role of co-deleted genes in the 1.4 Mb interval of type-1 deletions, and their possible implication in the main clinical features observed in this high-risk group of NF1 patients.
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Affiliation(s)
- Laurence Pacot
- Fédération de Génétique et Médecine Génomique, Hôpital Cochin, DMU BioPhyGen, AP-HP, Centre-Université Paris Cité, Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France
| | - Milind Girish
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Samantha Knight
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | - Vinod Varghese
- All Wales Medical Genomics Service, Cardiff, Great Britain
| | - Manuela Ye
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France
| | - Nick Thomas
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Eric Pasmant
- Fédération de Génétique et Médecine Génomique, Hôpital Cochin, DMU BioPhyGen, AP-HP, Centre-Université Paris Cité, Paris, France.
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France.
| | - Meena Upadhyaya
- Division of Cancer and Genetics, Institute of Medical Genetics, Cardiff University, Heath Park, CF14 4XN, Cardiff, UK
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2
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Wang D, Wen X, Xu LL, Chen QX, Yan TX, Xiao HT, Xu XW. Nf1 in heart development: a potential causative gene for congenital heart disease: a narrative review. Physiol Genomics 2023; 55:415-426. [PMID: 37519249 DOI: 10.1152/physiolgenomics.00024.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/26/2023] [Accepted: 07/08/2023] [Indexed: 08/01/2023] Open
Abstract
Congenital heart disease is the most frequent congenital disorder, affecting a significant number of live births. Gaining insights into its genetic etiology could lead to a deeper understanding of this condition. Although the Nf1 gene has been identified as a potential causative gene, its role in congenital heart disease has not been thoroughly clarified. We searched and summarized evidence from cohort-based and experimental studies on the issue of Nf1 and heart development in congenital heart diseases from various databases. Available evidence demonstrates a correlation between Nf1 and congenital heart diseases, mainly pulmonary valvar stenosis. The mechanism underlying this correlation may involve dysregulation of epithelial-mesenchymal transition (EMT). The Nf1 gene affects the EMT process via multiple pathways, including directly regulating the expression of EMT-related transcription factors and indirectly regulating the EMT process by regulating the MAPK pathway. This narrative review provides a comprehensive account of the Nf1 involvement in heart development and congenital cardiovascular diseases in terms of epidemiology and potential mechanisms. RAS signaling may contribute to congenital heart disease independently or in cooperation with other signaling pathways. Efficient management of both NF1 and cardiovascular disease patients would benefit from further research into these issues.
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Affiliation(s)
- Dun Wang
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, People's Republic of China
| | - Xue Wen
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, People's Republic of China
| | - Li-Li Xu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, People's Republic of China
| | - Qing-Xing Chen
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, People's Republic of China
| | - Tian-Xing Yan
- Central Laboratory, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, People's Republic of China
| | - Hai-Tao Xiao
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, People's Republic of China
| | - Xue-Wen Xu
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, People's Republic of China
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3
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Integrin-Dependent Regulation of Small GTPases: Role in Cell Migration. J Indian Inst Sci 2017. [DOI: 10.1007/s41745-016-0010-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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4
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Emerging genotype-phenotype relationships in patients with large NF1 deletions. Hum Genet 2017; 136:349-376. [PMID: 28213670 PMCID: PMC5370280 DOI: 10.1007/s00439-017-1766-y] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 02/08/2017] [Indexed: 02/07/2023]
Abstract
The most frequent recurring mutations in neurofibromatosis type 1
(NF1) are large deletions encompassing the NF1
gene and its flanking regions (NF1
microdeletions). The majority of these deletions encompass 1.4-Mb and are associated
with the loss of 14 protein-coding genes and four microRNA genes. Patients with
germline type-1 NF1 microdeletions frequently
exhibit dysmorphic facial features, overgrowth/tall-for-age stature, significant
delay in cognitive development, large hands and feet, hyperflexibility of joints and
muscular hypotonia. Such patients also display significantly more cardiovascular
anomalies as compared with patients without large deletions and often exhibit
increased numbers of subcutaneous, plexiform and spinal neurofibromas as compared
with the general NF1 population. Further, an extremely high burden of internal
neurofibromas, characterised by >3000 ml tumour volume, is encountered
significantly, more frequently, in non-mosaic NF1
microdeletion patients than in NF1 patients lacking such deletions. NF1 microdeletion patients also have an increased risk of
malignant peripheral nerve sheath tumours (MPNSTs); their lifetime MPNST risk is
16–26%, rather higher than that of NF1 patients with intragenic NF1 mutations (8–13%). NF1 microdeletion patients, therefore, represent a high-risk group for
the development of MPNSTs, tumours which are very aggressive and difficult to treat.
Co-deletion of the SUZ12 gene in addition to
NF1 further increases the MPNST risk in
NF1 microdeletion patients. Here, we summarise
current knowledge about genotype–phenotype relationships in NF1 microdeletion patients and discuss the potential role of the genes
located within the NF1 microdeletion interval
whose haploinsufficiency may contribute to the more severe clinical
phenotype.
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5
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Sundarrajan S, Arumugam M. Weighted gene co-expression based biomarker discovery for psoriasis detection. Gene 2016; 593:225-234. [PMID: 27523473 DOI: 10.1016/j.gene.2016.08.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 08/05/2016] [Accepted: 08/10/2016] [Indexed: 02/08/2023]
Abstract
Psoriasis is a chronic inflammatory disease of the skin with an unknown aetiology. The disease manifests itself as red and silvery scaly plaques distributed over the scalp, lower back and extensor aspects of the limbs. After receiving scant consideration for quite a few years, psoriasis has now become a prominent focus for new drug development. A group of closely connected and differentially co-expressed genes may act in a network and may serve as molecular signatures for an underlying phenotype. A weighted gene coexpression network analysis (WGCNA), a system biology approach has been utilized for identification of new molecular targets for psoriasis. Gene coexpression relationships were investigated in 58 psoriatic lesional samples resulting in five gene modules, clustered based on the gene coexpression patterns. The coexpression pattern was validated using three psoriatic datasets. 10 highly connected and informative genes from each module was selected and termed as psoriasis specific hub signatures. A random forest based binary classifier built using the expression profiles of signature genes robustly distinguished psoriatic samples from the normal samples in the validation set with an accuracy of 0.95 to 1. These signature genes may serve as potential candidates for biomarker discovery leading to new therapeutic targets. WGCNA, the network based approach has provided an alternative path to mine out key controllers and drivers of psoriasis. The study principle from the current work can be extended to other pathological conditions.
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Affiliation(s)
- Sudharsana Sundarrajan
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology University, India
| | - Mohanapriya Arumugam
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology University, India.
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Thompson A, Stephens JW, Bain SC, Kanamarlapudi V. Molecular Characterisation of Small Molecule Agonists Effect on the Human Glucagon Like Peptide-1 Receptor Internalisation. PLoS One 2016; 11:e0154229. [PMID: 27100083 PMCID: PMC4839733 DOI: 10.1371/journal.pone.0154229] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/11/2016] [Indexed: 01/23/2023] Open
Abstract
The glucagon-like peptide receptor (GLP-1R), which is a G-protein coupled receptor (GPCR), signals through both Gαs and Gαq coupled pathways and ERK phosphorylation to stimulate insulin secretion. The aim of this study was to determine molecular details of the effect of small molecule agonists, compounds 2 and B, on GLP-1R mediated cAMP production, intracellular Ca2+ accumulation, ERK phosphorylation and its internalisation. In human GLP-1R (hGLP-1R) expressing cells, compounds 2 and B induced cAMP production but caused no intracellular Ca2+ accumulation, ERK phosphorylation or hGLP-1R internalisation. GLP-1 antagonists Ex(9-39) and JANT-4 and the orthosteric binding site mutation (V36A) in hGLP-1R failed to inhibit compounds 2 and B induced cAMP production, confirming that their binding site distinct from the GLP-1 binding site on GLP-1R. However, K334A mutation of hGLP-1R, which affects Gαs coupling, inhibited GLP-1 as well as compounds 2 and B induced cAMP production, indicating that GLP-1, compounds 2 and B binding induce similar conformational changes in the GLP-1R for Gαs coupling. Additionally, compound 2 or B binding to the hGLP-1R had significantly reduced GLP-1 induced intracellular Ca2+ accumulation, ERK phosphorylation and hGLP-1R internalisation. This study illustrates pharmacology of differential activation of GLP-1R by GLP-1 and compounds 2 and B.
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Affiliation(s)
- Aiysha Thompson
- Institute of Life Science 1, Medical School, Swansea University, Singleton Park, Swansea, United Kingdom
| | - Jeffrey W. Stephens
- Institute of Life Science 1, Medical School, Swansea University, Singleton Park, Swansea, United Kingdom
| | - Stephen C. Bain
- Institute of Life Science 1, Medical School, Swansea University, Singleton Park, Swansea, United Kingdom
| | - Venkateswarlu Kanamarlapudi
- Institute of Life Science 1, Medical School, Swansea University, Singleton Park, Swansea, United Kingdom
- * E-mail:
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7
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Regulators and Effectors of Arf GTPases in Neutrophils. J Immunol Res 2015; 2015:235170. [PMID: 26609537 PMCID: PMC4644846 DOI: 10.1155/2015/235170] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 09/30/2015] [Indexed: 12/22/2022] Open
Abstract
Polymorphonuclear neutrophils (PMNs) are key innate immune cells that represent the first line of defence against infection. They are the first leukocytes to migrate from the blood to injured or infected sites. This process involves molecular mechanisms that coordinate cell polarization, delivery of receptors, and activation of integrins at the leading edge of migrating PMNs. These phagocytes actively engulf microorganisms or form neutrophil extracellular traps (NETs) to trap and kill pathogens with bactericidal compounds. Association of the NADPH oxidase complex at the phagosomal membrane for production of reactive oxygen species (ROS) and delivery of proteolytic enzymes into the phagosome initiate pathogen killing and removal. G protein-dependent signalling pathways tightly control PMN functions. In this review, we will focus on the small monomeric GTPases of the Arf family and their guanine exchange factors (GEFs) and GTPase activating proteins (GAPs) as components of signalling cascades regulating PMN responses. GEFs and GAPs are multidomain proteins that control cellular events in time and space through interaction with other proteins and lipids inside the cells. The number of Arf GAPs identified in PMNs is expanding, and dissecting their functions will provide important insights into the role of these proteins in PMN physiology.
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ADAP2 Is an Interferon Stimulated Gene That Restricts RNA Virus Entry. PLoS Pathog 2015; 11:e1005150. [PMID: 26372645 PMCID: PMC4570769 DOI: 10.1371/journal.ppat.1005150] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/13/2015] [Indexed: 12/19/2022] Open
Abstract
Interferon stimulated genes (ISGs) target viruses at various stages of their infectious life cycles, including at the earliest stage of viral entry. Here we identify ArfGAP with dual pleckstrin homology (PH) domains 2 (ADAP2) as a gene upregulated by type I IFN treatment in a STAT1-dependent manner. ADAP2 functions as a GTPase-activating protein (GAP) for Arf6 and binds to phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3) and PI(3,4)P2. We show that overexpression of ADAP2 suppresses dengue virus (DENV) and vesicular stomatitis virus (VSV) infection in an Arf6 GAP activity-dependent manner, while exerting no effect on coxsackievirus B (CVB) or Sendai virus (SeV) replication. We further show that ADAP2 expression induces macropinocytosis and that ADAP2 strongly associates with actin-enriched membrane ruffles and with Rab8a- and LAMP1-, but not EEA1- or Rab7-, positive vesicles. Utilizing two techniques--light-sensitive neutral red (NR)-containing DENV and fluorescence assays for virus internalization--we show that ADAP2 primarily restricts DENV infection at the stage of virion entry and/or intracellular trafficking and that incoming DENV and VSV particles associate with ADAP2 during their entry. Taken together, this study identifies ADAP2 as an ISG that exerts antiviral effects against RNA viruses by altering Arf6-mediated trafficking to disrupt viral entry.
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9
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Kanamarlapudi V. Exchange factor EFA6R requires C-terminal targeting to the plasma membrane to promote cytoskeletal rearrangement through the activation of ADP-ribosylation factor 6 (ARF6). J Biol Chem 2014; 289:33378-90. [PMID: 25296758 PMCID: PMC4246094 DOI: 10.1074/jbc.m113.534156] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
ADP-ribosylation factor 6 (ARF6) small GTPase regulates membrane trafficking and cytoskeleton rearrangements at the plasma membrane (PM) by cycling between the GTP-bound active and GDP-bound inactive conformations. Guanine nucleotide exchange factors (GEFs) activate ARF6. The exchange factor for ARF6 (EFA6) R has been identified as a biomarker for ovarian cancer. EFA6R shares the catalytic Sec7, pleckstrin homology (PH), and coiled coil (CC) domains of the other EFA6 family GEFs. Here we report the functional characterization of EFA6R. Endogenous EFA6R was present in the plasma membrane fraction. The exogenously expressed FLAG- and GFP-tagged EFA6R were targeted to the PM. In vitro, GFP-EFA6R associated weakly but preferentially with phosphatidylinositol 4,5-bisphosphate (PIP2) through the PH domain. EFA6R required both its PH and CC domains localized at the C terminus to target the PM. Consistent with this, EFA6R lacking the CC domain (EFA6RΔCC) was released from the PM into the cytosol upon PIP2 depletion, whereas EFA6R release from the PM required both PIP2 depletion and actin destabilization. These results suggest that the dual targeting via the PH and CC domains is important for the PM localization of EFA6R. EFA6R specifically catalyzed the GTP loading of ARF6 in mammalian cells. Moreover, EFA6R regulated ARF6 localization and thereby actin stress fiber loss. The GEF activity of EFA6R was dependent on the presence of the Sec7 domain. The PH and CC domains were also required for the in vivo GEF activity of EFA6R but could be functionally replaced by the CAAX motif of K-Ras, suggesting a role for these domains in the membrane targeting of EFA6R.
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Affiliation(s)
- Venkateswarlu Kanamarlapudi
- From the Institute of Life Science 1, College of Medicine, Swansea University, Singleton Park, Swansea SA2 8PP, United Kingdom
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10
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Venturin M, Carra S, Gaudenzi G, Brunelli S, Gallo GR, Moncini S, Cotelli F, Riva P. ADAP2 in heart development: a candidate gene for the occurrence of cardiovascular malformations in NF1 microdeletion syndrome. J Med Genet 2014; 51:436-43. [PMID: 24711647 DOI: 10.1136/jmedgenet-2013-102240] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Cardiovascular malformations have a higher incidence in patients with NF1 microdeletion syndrome compared to NF1 patients with intragenic mutation, presumably owing to haploinsufficiency of one or more genes included in the deletion interval and involved in heart development. In order to identify which genes could be responsible for cardiovascular malformations in the deleted patients, we carried out expression studies in mouse embryos and functional studies in zebrafish. METHODS AND RESULTS The expression analysis of three candidate genes included in the NF1 deletion interval, ADAP2, SUZ12 and UTP6, performed by in situ hybridisation, showed the expression of ADAP2 murine ortholog in heart during fundamental phases of cardiac morphogenesis. In order to investigate the role of ADAP2 in cardiac development, we performed loss-of-function experiments of zebrafish ADAP2 ortholog, adap2, by injecting two different morpholino oligos (adap2-MO and UTR-adap2-MO). adap2-MOs-injected embryos (morphants) displayed in vivo circulatory and heart shape defects. The molecular characterisation of morphants with cardiac specific markers showed that the injection of adap2-MOs causes defects in heart jogging and looping. Additionally, morphological and molecular analysis of adap2 morphants demonstrated that the loss of adap2 function leads to defective valvulogenesis, suggesting a correlation between ADAP2 haploinsufficiency and the occurrence of valve defects in NF1-microdeleted patients. CONCLUSIONS Overall, our findings indicate that ADAP2 has a role in heart development, and might be a reliable candidate gene for the occurrence of cardiovascular malformations in patients with NF1 microdeletion and, more generally, for the occurrence of a subset of congenital heart defects.
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Affiliation(s)
- Marco Venturin
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Silvia Carra
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Germano Gaudenzi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Silvia Brunelli
- Dipartimento di Scienze della Salute, Università degli Studi di Milano-Bicocca, Monza (MB), Italy
| | | | - Silvia Moncini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Franco Cotelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Paola Riva
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
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Kanai Y, Wang D, Hirokawa N. KIF13B enhances the endocytosis of LRP1 by recruiting LRP1 to caveolae. ACTA ACUST UNITED AC 2014; 204:395-408. [PMID: 24469637 PMCID: PMC3912526 DOI: 10.1083/jcb.201309066] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The motor protein KIF13B has an unconventional role as a scaffold that recruits lipoprotein receptor–related protein 1 to caveolae, thereby enhancing its endocytosis. Multifunctional low-density lipoprotein (LDL) receptor-related protein 1 (LRP1) recognizes and internalizes a large number of diverse ligands, including LDL and factor VIII. However, little is known about the regulation of LRP1 endocytosis. Here, we show that a microtubule-based motor protein, KIF13B, in an unexpected and unconventional function, enhances caveolin-dependent endocytosis of LRP1. KIF13B was highly expressed in the liver and was localized on the sinusoidal plasma membrane of hepatocytes. KIF13B knockout (KO) mice showed elevated levels of serum cholesterol and factor VIII, and KO MEFs showed decreased uptake of LDL. Exogenous KIF13B, initially localized on the plasma membrane with caveolae, was translocated to the vesicles in the cytoplasm with LRP1 and caveolin-1. KIF13B bound to hDLG1 and utrophin, which, in turn, bound to LRP1 and caveolae, respectively. These linkages were required for the KIF13B-enhanced endocytosis of LRP1. Thus, we propose that KIF13B, working as a scaffold, recruits LRP1 to caveolae via LRP1–hDLG1–KIF13B–utrophin–caveolae linkage and enhances the endocytosis of LRP1.
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Affiliation(s)
- Yoshimitsu Kanai
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
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12
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Oikawa T, Kuroda Y, Matsuo K. Regulation of osteoclasts by membrane-derived lipid mediators. Cell Mol Life Sci 2013; 70:3341-53. [PMID: 23296124 PMCID: PMC3753467 DOI: 10.1007/s00018-012-1238-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 12/05/2012] [Accepted: 12/10/2012] [Indexed: 12/22/2022]
Abstract
Osteoclasts are bone-resorbing cells of monocytic origin. An imbalance between bone formation and resorption can lead to osteoporosis or osteopetrosis. Osteoclastogenesis is triggered by RANKL- and IP3-induced Ca2+ influx followed by activation of NFATc1, a master transcription factor for osteoclastogenic gene regulation. During differentiation, osteoclasts undergo cytoskeletal remodeling to migrate and attach to the bone surface. Simultaneously, they fuse with each other to form multinucleated cells. These processes require PI3-kinase-dependent cytoskeletal protein activation to initiate cytoskeletal remodeling, resulting in the formation of circumferential podosomes and fusion-competent protrusions. In multinucleated osteoclasts, circumferential podosomes mature into stabilized actin rings, which enables the formation of a ruffled border where intensive membrane trafficking is executed. Membrane lipids, especially phosphoinositides, are key signaling molecules that regulate osteoclast morphology and act as second messengers and docking sites for multiple important effectors. We examine the critical roles of phosphoinositides in the signaling cascades that regulate osteoclast functions.
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Affiliation(s)
- Tsukasa Oikawa
- Laboratory of Cell and Tissue Biology, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo, 160-8582, Japan.
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Zuccotti P, Cartelli D, Stroppi M, Pandini V, Venturin M, Aliverti A, Battaglioli E, Cappelletti G, Riva P. Centaurin-α₂ interacts with β-tubulin and stabilizes microtubules. PLoS One 2012; 7:e52867. [PMID: 23285209 PMCID: PMC3527619 DOI: 10.1371/journal.pone.0052867] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 11/23/2012] [Indexed: 01/01/2023] Open
Abstract
Centaurin-α₂ is a GTPase-activating protein for ARF (ARFGAP) showing a diffuse cytoplasmic localization capable to translocate to membrane, where it binds phosphatidylinositols. Taking into account that Centaurin-α₂ can localize in cytoplasm and that its cytoplasmatic function is not well defined, we searched for further interactors by yeast two-hybrid assay to investigate its biological function. We identified a further Centaurin-α₂ interacting protein, β-Tubulin, by yeast two-hybrid assay. The interaction, involving the C-terminal region of β-Tubulin, has been confirmed by coimmunoprecipitation experiments. After Centaurin-α₂ overexpression in HeLa cells and extraction of soluble (αβ dimers) and insoluble (microtubules) fractions of Tubulin, we observed that Centaurin-α₂ mainly interacts with the polymerized Tubulin fraction, besides colocalizing with microtubules (MTs) in cytoplasm accordingly. Even following the depolimerizing Tubulin treatments Centaurin-α₂ remains mainly associated to nocodazole- and cold-resistant MTs. We found an increase of MT stability in transfected HeLa cells, evaluating as marker of stability the level of MT acetylation. In vitro assays using purified Centaurin-α₂ and tubulin confirmed that Centaurin-α₂ promotes tubulin assembly and increases microtubule stability. The biological effect of Centaurin-α₂ overexpression, assessed through the detection of an increased number of mitotic HeLa cells with bipolar spindles and with the correct number of centrosomes in both dividing and not dividing cells, is consistent with the Centaurin-α₂ role on MT stabilization. Centaurin-α₂ interacts with β-Tubulin and it mainly associates to MTs, resistant to destabilizing agents, in vitro and in cell. We propose Centaurin-α₂ as a new microtubule-associated protein (MAP) increasing MT stability.
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Affiliation(s)
- Paola Zuccotti
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milano, Italy
| | - Daniele Cartelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Michela Stroppi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milano, Italy
| | - Vittorio Pandini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Marco Venturin
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milano, Italy
| | | | - Elena Battaglioli
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milano, Italy
| | | | - Paola Riva
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milano, Italy
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Hu Z, Du J, Yang L, Zhu Y, Yang Y, Zheng D, Someya A, Gu L, Lu X. GEP100/Arf6 is required for epidermal growth factor-induced ERK/Rac1 signaling and cell migration in human hepatoma HepG2 cells. PLoS One 2012; 7:e38777. [PMID: 22701712 PMCID: PMC3372492 DOI: 10.1371/journal.pone.0038777] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 05/10/2012] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Epidermal growth factor (EGF) signaling is implicated in the invasion and metastasis of hepatoma cells. However, the signaling pathways for EGF-induced motility of hepatoma cells remain undefined. METHODOLOGY/PRINCIPAL FINDINGS We found that EGF dose-dependently stimulated the migration of human hepatoma cells HepG2, with the maximal effect at 10 ng/mL. Additionally, EGF increased Arf6 activity, and ectopic expression of Arf6 T27N, a dominant negative Arf6 mutant, largely abolish EGF-induced cell migration. Blocking GEP100 with GEP100 siRNA or GEP100-△PH, a pleckstrin homology (PH) domain deletion mutant of GEP100, blocked EGF-induced Arf6 activity and cell migration. EGF also increased ERK and Rac1 activity. Ectopic expression GEP100 siRNA, GEP100-△PH, or Arf6-T27N suppressed EGF-induced ERK and Rac1 activity. Furthermore, blocking ERK signaling with its inhibitor U0126 remarkably inhibited both EGF-induced Rac1 activation as well as cell migration, and ectopic expression of inactive mutant form of Rac1 (Rac1-T17N) also largely abolished EGF-induced cell migration. CONCLUSIONS/SIGNIFICANCE Taken together, this study highlights the function of the PH domain of GEP100 and its regulated Arf6/ERK/Rac1 signaling cascade in EGF-induced hepatoma cell migration. These findings could provide a rationale for designing new therapy based on inhibition of hepatoma metastasis.
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Affiliation(s)
- ZhenZhen Hu
- Department of Physiology, Nanjing Medical University, Nanjing, China
- Department of Pediatrics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jun Du
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Ling Yang
- Department of Cardiology, The Third Affiliated Hospital of Suzhou University, Suzhou, China
| | - YiChao Zhu
- Department of Physiology, Nanjing Medical University, Nanjing, China
| | - Yu Yang
- Department of Physiology, Nanjing Medical University, Nanjing, China
| | - DaTong Zheng
- Department of Pediatrics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Akimasa Someya
- Department of Host Defense and Biochemical Research, Juntendo University School of Medicine, Tokyo, Japan
| | - Luo Gu
- Cancer Center, Nanjing Medical University, Nanjing, China
- * E-mail: (LG); (XL)
| | - Xiang Lu
- Department of Geriatrics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
- * E-mail: (LG); (XL)
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Kanamarlapudi V, Owens SE, Lartey J, López Bernal A. ADP-ribosylation factor 6 expression and activation are reduced in myometrium in complicated pregnancies. PLoS One 2012; 7:e37954. [PMID: 22666423 PMCID: PMC3364193 DOI: 10.1371/journal.pone.0037954] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 04/27/2012] [Indexed: 12/31/2022] Open
Abstract
Background ARF6 (ADP-ribosylation factor 6) small GTP binding protein plays critical roles in actin cytoskeleton rearrangements and membrane trafficking, including internalisation of G protein coupled receptors (GPCR). ARF6 operates by cycling between GDP-bound (inactive) and GTP-bound (active) forms and is a potential regulator of GPCR-mediated uterine activity during pregnancy and labour. ARF6 contains very low intrinsic GTP binding activity and depends on GEFs (guanine nucleotide exchange factors) such as CYTH3 (cytohesin 3) to bind GTP. ARF6 and CYTH3 were originally cloned from human placenta, but there is no information on their expression in other reproductive tissues. Methods The expression of ARF6, ARF1, and CYTH1-4 was investigated by measuring mRNA (using RT-PCR) and protein levels (using immunoblotting) in samples of myometrium obtained from non-pregnant women, and women with normal pregnancies, before or after the spontaneous onset of labour. We also analysed myometrial samples from women with spontaneous preterm labour and from women with complicated pregnancies requiring emergency preterm delivery. The GST)-effector pull down assay was used to study the presence of active ARF6 and ARF1 in all myometrial extracts. Results ARF6, ARF1 and CYTH3 but not CYTH1, CYTH2 and CYTH4 were expressed in all samples and the levels did not change with pregnancy or labour. However, ARF6 and CYTH3 but not ARF1 levels were significantly reduced in complicated pregnancies. The alterations in the expression of ARF6 and its GEF in human myometrium indicate a potential involvement of this signalling system in modulating the response of myometrial smooth muscle in complicated pregnancies. The levels of ARF6-GTP or ARF1-GTP did not change with pregnancy or labour but ARF6-GTP levels were significantly decreased in women with severe complications of pregnancy. Conclusions We have demonstrated a functional ARF6 system in human myometrium and a correlation between ARF6 level and activity in uterine and abnormal pregnancy.
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Affiliation(s)
- Venkateswarlu Kanamarlapudi
- Institute of Life Science, College of Medicine, Swansea University, Swansea, United Kingdom
- * E-mail: (VK); (ALB)
| | - Sian E. Owens
- Institute of Life Science, College of Medicine, Swansea University, Swansea, United Kingdom
| | - Jon Lartey
- Division of Obstetrics and Gynaecology, School of Clinical Sciences, University of Bristol, Bristol, United Kingdom
| | - Andrés López Bernal
- Division of Obstetrics and Gynaecology, School of Clinical Sciences, University of Bristol, Bristol, United Kingdom
- * E-mail: (VK); (ALB)
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Sircar A, Chaudhury S, Kilambi KP, Berrondo M, Gray JJ. A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19. Proteins 2011; 78:3115-23. [PMID: 20535822 DOI: 10.1002/prot.22765] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In CAPRI rounds 13-19, the most native-like structure predicted by RosettaDock resulted in two high, one medium, and one acceptable accuracy model out of 13 targets. The current rounds of CAPRI were especially challenging with many unbound and homology modeled starting structures. Novel docking methods, including EnsembleDock and SnugDock, allowed backbone conformational sampling during docking and enabled the creation of more accurate models. For Target 32, α-amylase/subtilisin inhibitor-subtilisin savinase, we sampled different backbone conformations at an interfacial loop to produce five high-quality models including the most accurate structure submitted in the challenge (2.1 Å ligand rmsd, 0.52 Å interface rmsd). For Target 41, colicin-immunity protein, we used EnsembleDock to sample the ensemble of nuclear magnetic resonance (NMR) models of the immunity protein to generate a medium accuracy structure. Experimental data identifying the catalytic residues at the binding interface for Target 40 (trypsin-inhibitor) were used to filter RosettaDock global rigid body docking decoys to determine high accuracy predictions for the two distinct binding sites in which the inhibitor interacts with trypsin. We discuss our generalized approach to selecting appropriate methods for different types of docking problems. The current toolset provides some robustness to errors in homology models, but significant challenges remain in accommodating larger backbone uncertainties and in sampling adequately for global searches.
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Affiliation(s)
- Aroop Sircar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
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Pasmant E, Masliah-Planchon J, Lévy P, Laurendeau I, Ortonne N, Parfait B, Valeyrie-Allanore L, Leroy K, Wolkenstein P, Vidaud M, Vidaud D, Bièche I. Identification of genes potentially involved in the increased risk of malignancy in NF1-microdeleted patients. Mol Med 2010; 17:79-87. [PMID: 20844836 DOI: 10.2119/molmed.2010.00079] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 09/07/2010] [Indexed: 11/06/2022] Open
Abstract
Patients with NF1 microdeletion develop more neurofibromas at a younger age, and have an increased risk of malignant peripheral nerve sheath tumors (MPNSTs). We postulated that the increased risk of malignancy could be due to inactivation, in addition to NF1, of a second tumor suppressor gene located in the typical 1.4-Mb microdeletion found in most of the microdeleted patients. We investigated the expression of NF1, the other 16 protein-coding genes and the 2 microRNAs located in the 1.4-Mb microdeletion by means of real-time quantitative reverse-transcription polymerase chain reaction (RT-PCR) in a large series of human dermal and plexiform neurofibromas and MPNSTs. Five genes were significantly upregulated: OMG and SUZ12 in plexiform neurofibromas and ATAD5, EVI2A and C17orf79 in MPNSTs. More interestingly, two genes were significantly downregulated (RNF135 and CENTA2) in tumor Schwann cells from MPNST biopsies and in MPNST cell lines. This study points to the involvement of several genes (particularly RNF135 and CENTA2) in the increased risk of malignancy observed in NF1-microdeleted patients.
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Affiliation(s)
- Eric Pasmant
- Université Paris Descartes, Faculté des Sciences Pharmaceutiques et Biologiques, Paris, France.
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Whitney TJ, Gardner DG, Mott ML, Brandon M. Identifying the molecular basis of functions in the transcriptome of the social amoeba Dictyostelium discoideum. GENETICS AND MOLECULAR RESEARCH 2010; 9:394-415. [PMID: 20309825 DOI: 10.4238/vol9-1gmr752] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The unusual life cycle of Dictyostelium discoideum, in which an extra-cellular stressor such as starvation induces the development of a multicellular fruiting body consisting of stalk cells and spores from a culture of identical amoebae, provides an excellent model for investigating the molecular control of differentiation and the transition from single- to multi-cellular life, a key transition in development. We utilized serial analysis of gene expression (SAGE), a molecular method that is unbiased by dependence on previously identified genes, to obtain a transcriptome from a high-density culture of amoebae, in order to examine the transition to multi-cellular development. The SAGE method provides relative expression levels, which allows us to rank order the expressed genes. We found that a large number of ribosomal proteins were expressed at high levels, while various components of the proteosome were expressed at low levels. The only identifiable transmembrane signaling system components expressed in amoebae are related to quorum sensing, and their expression levels were relatively low. The most highly expressed gene in the amoeba transcriptome, dutA untranslated RNA, is a molecule with unknown function that may serve as an inhibitor of translation. These results suggest that high-density amoebae have not initiated development, and they also suggest a mechanism by which the transition into the development program is controlled.
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Affiliation(s)
- T J Whitney
- Department of Biological Sciences, Idaho State University, Pocatello, ID, USA
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Vashisht AA, Kennedy PJ, Russell P. Centaurin-like protein Cnt5 contributes to arsenic and cadmium resistance in fission yeast. FEMS Yeast Res 2009; 9:257-69. [PMID: 19076239 PMCID: PMC2820371 DOI: 10.1111/j.1567-1364.2008.00467.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Arsenic (As) and cadmium (Cd) are two of the most hazardous substances in the environment and have been implicated in a number of human diseases including cancer. Their mechanisms of toxicity and subsequent carcinogenesis are not understood. To identify the genes involved in As/Cd detoxification, we screened a random insertional mutagenesis library of Schizosaccharomyces pombe for mutants that are hypersensitive to As/Cd. Mutations were mapped to spc1(+) (sty1(+)) and SPBC17G9.08c. Spc1 is a stress-activated protein kinase orthologous to human p38. A fragment of SPBC17G9.08c was previously identified as csx2, a high-copy suppressor of cut6 that encodes an acetyl-CoA carboxylase involved in fatty acid biosynthesis. SPBC17G9.08c is a member of the centaurin ADP ribosylation factor GTPase activating protein family found in a variety of fungi, plants and metazoans, but not in Saccharomyces cerevisiae. Cnt5, so named because its closest human homolog is centaurin beta-5, binds to phosphatidic acid and phosphatidyl serine in vitro. Microscopic localization of Cnt5-GFP indicates significant redistribution of Cnt5 from the cytoplasm to the cell membranes in response to As stress. These data suggest a model in which Cnt5 contributes to As/Cd resistance by maintaining membrane integrity or by modulating membrane trafficking.
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Affiliation(s)
- Ajay Amar Vashisht
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037. U.S.A
| | - Patrick Joseph Kennedy
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037. U.S.A
| | - Paul Russell
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037. U.S.A
- Department of Cell Biology, The Scripps Research Institute, La Jolla, California 92037. U.S.A
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Wang H, Ma J, Ruan L, Xu X. Cloning of a centaurin-alpha1 like gene MjCent involved in WSSV infection from shrimp Marsupeneaus japonicus. FISH & SHELLFISH IMMUNOLOGY 2009; 26:279-284. [PMID: 19073266 DOI: 10.1016/j.fsi.2008.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2008] [Revised: 10/22/2008] [Accepted: 10/28/2008] [Indexed: 05/27/2023]
Abstract
Centaurin-alpha1 specifically binds phosphatidylinositol 3,4,5-trisphosphate (PI (3,4,5)P3) and is a GTPase-activating protein (GAP) of ADP-ribosylation factor (ARF6). It actively engages in phosphatidylinositol 3-kinase (PI3-K) mediated cell signal transduction. Here, for the first time, we have identified a virus related centaurin-alpha1 homologue named MjCent from the shrimp, Marsupeneaus japonicus, an economically important crustacean in the aquaculture industry. MjCent has one conserved ArfGAP and two Pleckstrin homology domains (PH domains). As shown by RT-PCR and immunofluorescence, MjCent appeared in every tissue examined and was localized mainly in the cell cytoplasm. Further investigation with real-time quantitative PCR showed that MjCent was significantly up-regulated during white spot syndrome virus (WSSV) infection, but notably decreased in virus-resistant shrimps. This suggests a close relationship between MjCent and WSSV invasion and host defense of the shrimp, M. japonicus.
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Affiliation(s)
- Huifen Wang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, Xiamen, 361005, PR China
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Expression analysis of genes lying in the NF1 microdeletion interval points to four candidate modifiers for neurofibroma formation. Neurogenetics 2008; 10:79-85. [PMID: 18850118 DOI: 10.1007/s10048-008-0154-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Accepted: 09/23/2008] [Indexed: 12/14/2022]
Abstract
The hallmark of neurofibromatosis type 1 (NF1) are multiple dermal neurofibromas. They show high inter- and intrafamilial variability for which the influence of modifying genes is discussed. NF1 patients presenting microdeletions spanning NF1 and several contiguous genes have an earlier onset and higher number of dermal neurofibromas than classical NF1 patients, pointing to one of the deleted genes as modifier. Expression analysis of 13 genes of the microdeletion region in dermal neurofibromas and other tissues revealed four candidates for the modification of neurofibroma formation: CENTA2, RAB11FIP4, C17orf79, and UTP6.
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Marshansky V, Futai M. The V-type H+-ATPase in vesicular trafficking: targeting, regulation and function. Curr Opin Cell Biol 2008; 20:415-26. [PMID: 18511251 PMCID: PMC7111286 DOI: 10.1016/j.ceb.2008.03.015] [Citation(s) in RCA: 374] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Revised: 03/27/2008] [Accepted: 03/31/2008] [Indexed: 12/31/2022]
Abstract
Vacuolar-type H+-ATPase (V-ATPase)-driven proton pumping and organellar acidification is essential for vesicular trafficking along both the exocytotic and endocytotic pathways of eukaryotic cells. Deficient function of V-ATPase and defects of vesicular acidification have been recently recognized as important mechanisms in a variety of human diseases and are emerging as potential therapeutic targets. In the past few years, significant progress has been made in our understanding of function, regulation, and the cell biological role of V-ATPase. Here, we will review these studies with emphasis on novel direct roles of V-ATPase in the regulation of vesicular trafficking events.
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Affiliation(s)
- Vladimir Marshansky
- Program in Membrane Biology, Center for Systems Biology, Simches Research Center, CPZN No. 8212, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.
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Rojas-Cartagena C, Ortíz-Pineda P, Ramírez-Gómez F, Suárez-Castillo EC, Matos-Cruz V, Rodríguez C, Ortíz-Zuazaga H, García-Arrarás JE. Distinct profiles of expressed sequence tags during intestinal regeneration in the sea cucumber Holothuria glaberrima. Physiol Genomics 2007; 31:203-15. [PMID: 17579180 PMCID: PMC2866185 DOI: 10.1152/physiolgenomics.00228.2006] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Repair and regeneration are key processes for tissue maintenance, and their disruption may lead to disease states. Little is known about the molecular mechanisms that underline the repair and regeneration of the digestive tract. The sea cucumber Holothuria glaberrima represents an excellent model to dissect and characterize the molecular events during intestinal regeneration. To study the gene expression profile, cDNA libraries were constructed from normal, 3-day, and 7-day regenerating intestines of H. glaberrima. Clones were randomly sequenced and queried against the nonredundant protein database at the National Center for Biotechnology Information. RT-PCR analyses were made of several genes to determine their expression profile during intestinal regeneration. A total of 5,173 sequences from three cDNA libraries were obtained. About 46.2, 35.6, and 26.2% of the sequences for the normal, 3-days, and 7-days cDNA libraries, respectively, shared significant similarity with known sequences in the protein database of GenBank but only present 10% of similarity among them. Analysis of the libraries in terms of functional processes, protein domains, and most common sequences suggests that a differential expression profile is taking place during the regeneration process. Further examination of the expressed sequence tag dataset revealed that 12 putative genes are differentially expressed at significant level (R > 6). Experimental validation by RT-PCR analysis reveals that at least three genes (unknown C-4677-1, melanotransferrin, and centaurin) present a differential expression during regeneration. These findings strongly suggest that the gene expression profile varies among regeneration stages and provide evidence for the existence of differential gene expression.
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